The complete set of genes and their genomic locations
could be identified via genomic sequencing with an acceptable investment.
A 1.35 Mb contiguous region consisting of 14 BAC/ PAC clones were anchored
on the long arm of chromosome 9 corresponding to about 15.5 cM of the
genetic map using sequence of DNA markers on the genetic map as well as
the EST markers. Candidate genes underlying major quantitative trait loci
(QTL) for submergence tolerance on chromosome 9 were identified 1.35 Mbp
from O. sativa subsp. japonica cv. Nipponbare. We predicted
a total of 228 CDS features on the submergence tolerance region, of which
104 are related to transposable elements (TEs). A putative function could
be assigned to 21 genes, with another 51 genes annotated as expressed,
leaving 71 that encode hypothetical proteins. On the basis of these finding,
the gene density with none transposable element-related gene in the critical
region of submergence tolerance is about 10.8 Kb/gene.